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- PDB-6f34: Crystal structure of a bacterial cationic amino acid transporter ... -

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Basic information

Entry
Database: PDB / ID: 6f34
TitleCrystal structure of a bacterial cationic amino acid transporter (CAT) homologue bound to Arginine.
Components
  • Amino acid transporter
  • MgtS
KeywordsMEMBRANE PROTEIN / Amino Acid Transporter / SLC7
Function / homology
Function and homology information


cellular response to magnesium starvation / transmembrane transporter activity / membrane / plasma membrane
Similarity search - Function
Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
ARGININE / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Small protein MgtS / Amino acid transporter
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsJungnickel, K.E.J. / Newstead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for amino acid transport by the CAT family of SLC7 transporters.
Authors: Jungnickel, K.E.J. / Parker, J.L. / Newstead, S.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid transporter
C: MgtS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8996
Polymers52,6242
Non-polymers1,2754
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Transporter is a heterodimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-21 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.037, 82.699, 118.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Amino acid transporter /


Mass: 49658.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK0930, ApcT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5L1G5
#2: Protein/peptide MgtS


Mass: 2965.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yneM, b4599, JW1527.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A5A616

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Non-polymers , 4 types, 78 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase / pH: 4
Details: 28-34 % PEG 400, 0.1 M sodium acetate pH 4.0 and 0.1 M potassium fluoride, containing 10 mM of the amino acid ligand.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.13→64.63 Å / Num. obs: 13951 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 94.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.074 / Rrim(I) all: 0.188 / Net I/σ(I): 5.5 / Num. measured all: 89902 / Scaling rejects: 84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.13-3.216.31.45210320.6790.6181.58199.8
14-64.635.10.0361950.9980.0210.04299.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12-2829-000refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQT

5oqt


Resolution: 3.13→50.926 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62
RfactorNum. reflection% reflection
Rfree0.2619 799 5.76 %
Rwork0.2312 --
obs0.233 13867 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.42 Å2 / Biso mean: 99.082 Å2 / Biso min: 55.19 Å2
Refinement stepCycle: final / Resolution: 3.13→50.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 80 74 3853
Biso mean--112.58 84.88 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023874
X-RAY DIFFRACTIONf_angle_d0.4745279
X-RAY DIFFRACTIONf_chiral_restr0.036633
X-RAY DIFFRACTIONf_plane_restr0.003638
X-RAY DIFFRACTIONf_dihedral_angle_d9.3552241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.13-3.32610.34041290.31932133226299
3.3261-3.58290.35791310.283221312262100
3.5829-3.94330.30231260.25421562282100
3.9433-4.51360.3021320.220721722304100
4.5136-5.68550.25381380.216221862324100
5.6855-50.93230.20251430.20972290243399
Refinement TLS params.Method: refined / Origin x: -12.3337 Å / Origin y: -1.9101 Å / Origin z: 25.4411 Å
111213212223313233
T0.974 Å2-0.0818 Å2-0.029 Å2-0.7464 Å20.0584 Å2--0.4859 Å2
L1.2133 °2-0.2033 °2-0.0972 °2-2.1688 °20.6838 °2--0.7378 °2
S0.1126 Å °0.0211 Å °-0.0752 Å °-0.2738 Å °-0.0533 Å °0.1259 Å °0.2474 Å °-0.2407 Å °-0.0506 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 461
2X-RAY DIFFRACTION1allB2
3X-RAY DIFFRACTION1allC1 - 27
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE12 - 13
6X-RAY DIFFRACTION1allW1 - 98

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